plot_umi_per_cell: Plot a histogram of the number of UMIs per cell with an...

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Plot a histogram of the number of UMIs per cell with an optional vertical line showing the cutoff for outliers.

Description

If max_zscore is specified, then there is both a high and a low cutoff, both of which are determined by Z-scoring the log-transformed UMI counts. Otherwise if min_rna_umi is specified, then there is only a low cutoff. If neither is specified, then no cutoff is shown.

Usage

plot_umi_per_cell(cds, max_zscore = NULL, min_rna_umi = NULL)

Arguments

cds	A cell_data_set for plotting.
max_zscore	Cutoff for the maximum Z-score of the log-transformed UMIs per cell. If NULL, then min_rna_umi must be specified.
min_rna_umi	Cutoff for the minimum number of UMIs per cell. Ignored if max_zscore is specified.

Value

A ggplot2 object.

cole-trapnell-lab/monocle3 documentation built on June 11, 2025, 11:22 p.m.